In the related art, there are known microscope systems for performing so-called time-lapse observation in which images of a sample are acquired by photographing the sample at a certain time interval (for example, see Patent Literature 1). With the microscope system disclosed in Patent Literature 1, Z-positions that serve as references for individual objective lenses are independently detected while moving the focal plane in the Z-axis direction, that is, the optical-axis direction, in a large area before starting observation or at the time of starting observation. Then, time-lapse observation is performed by changing the Z-position that serves as a reference in accordance with the objective lens to be used.